Proteome Discoverer Version 1.4

Xcalibur Proteome Discoverer Version 1.4 Installation Guide XCALI-97507 Revision A December 2012

2012 Thermo Fisher Scientific Inc. All rights reserved. Xcalibur is a registered trademark of Thermo Fisher Scientific Inc. in the United States. Proteome Discoverer is a trademark of Thermo Fisher Scientific Inc. in the United States. Firefox is a registered trademark of Mozilla Foundation in the United States. Excel, Internet Explorer, Microsoft, Visual C++, and Windows are registered trademarks of Microsoft Corporation in the United States and other countries. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc. The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser. Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly. This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents. Release history: Revision A, December 2012 Software Version: Thermo Proteome Discoverer version 1.4, Mascot Server 2.1 and later For Research Use Only. Not for use in diagnostic procedures.

C Contents Preface...............................................................v Related Documentation........................................... v System Requirements.............................................vi Special Notices..................................................vi Contacting Us................................................. vii Chapter 1 Installing Proteome Discoverer..........................................1 Opening the XInstall Window...................................... 1 Installing the Proteome Discoverer Software with an Internet Connection..... 2 Installing the Proteome Discoverer Software Without an Internet Connection.................................................. 16 Chapter 2 Installing Proteome Discoverer Daemon.................................19 Opening the XInstall Window..................................... 19 Installing the Proteome Discoverer Daemon Software.................... 20 Chapter 3 Installing Proteome Discoverer Viewer..................................31 Opening the XInstall Window..................................... 31 Installing the Proteome Discoverer Viewer Software..................... 32 Chapter 4 Connecting to the Mascot Server........................................43 Mascot Server Versions Supported................................... 43 Checking Your Mascot Server Settings............................... 44 Checking the URL............................................ 44 Checking for Security Options................................... 44 Configuring Mascot............................................. 45 Testing the Connection to the Mascot Server.......................... 47 Chapter 5 Submitting a Product Change Request...................................49 Index................................................................51 Thermo Scientific Proteome Discoverer Installation Guide iii

P Preface This guide describes how to install the Thermo Proteome Discoverer 1.4 application for peptide and protein mass spectrometry analyses. Contents Related Documentation System Requirements Special Notices Contacting Us To provide us with comments about this document, click the link below. Thank you in advance for your help. Related Documentation In addition to this installation guide, the Proteome Discoverer application includes Help and the Proteome Discoverer User Guide as a PDF file. To view product manuals Proteome Discoverer User Guide: Go to Start > Programs > Thermo Proteome Discoverer > Proteome Discoverer 1.4 User Guide or Help > User Guide. Proteome Discoverer Installation Guide: Go to Start > Programs > Thermo Proteome Discoverer > Proteome Discoverer 1.4 Installation Guide or Help > Installation Guide. To open Help From the Proteome Discoverer window, choose Help > Help Contents. If available for a specific window or view, click Help or press F1 for information about setting parameters. Thermo Scientific Proteome Discoverer Installation Guide v

Preface For more information, visit www.thermo.com. System Requirements The Proteome Discoverer application requires a license. In addition, your system must meet these minimum requirements. System Hardware Software Requirements 2 GHz processor with 2 GB RAM DVD/R-ROM drive Video card and monitor capable of 1280 1024 resolution (XGA) Screen resolution of 96 dpi 75 GB available on drive C NTFS format Microsoft Windows XP 32/64 Professional (English version) with latest service pack installed Microsoft Windows 7 32/64 Professional (English version) IMPORTANT Ensure that port 28199 is not blocked by firewalls. Note Ensure that the Windows operating system has the latest Microsoft.NET Framework and Windows updates installed before installing the Proteome Discoverer application. Special Notices Make sure you follow the precautionary statements presented in this guide. Special notices appear in boxes. IMPORTANT Highlights information necessary to prevent damage to software, loss of data, or invalid test results; or might contain information that is critical for optimal performance of the system. Note Highlights information of general interest. Tip Highlights helpful information that can make a task easier. vi Proteome Discoverer Installation Guide Thermo Scientific

Preface Running H/F 2 Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need. To contact Technical Support Phone 800-532-4752 Fax 561-688-8736 E-mail us.techsupport.analyze@thermofisher.com Knowledge base www.thermokb.com Find software updates and utilities to download at mssupport.thermo.com. To contact Customer Service for ordering information Phone 800-532-4752 Fax 561-688-8731 E-mail us.customer-support.analyze@thermofisher.com Web site www.thermo.com/ms To get local contact information for sales or service Go to www.thermoscientific.com/wps/portal/ts/contactus. To copy manuals from the Internet Go to mssupport.thermo.com, agree to the Terms and Conditions, and then click Customer Manuals in the left margin of the window. To suggest changes to documentation or to Help Fill out a reader survey online at www.surveymonkey.com/s/pqm6p62. Send an e-mail message to the Technical Publications Editor at techpubs-lcms@thermofisher.com. Thermo Scientific Proteome Discoverer Installation Guide vii

1 Installing Proteome Discoverer This guide describes how to install the Proteome Discoverer 1.4 software. Contents Opening the XInstall Window Installing the Proteome Discoverer Software with an Internet Connection Installing the Proteome Discoverer Software Without an Internet Connection Opening the XInstall Window Before you can access the Proteome Discoverer InstallShield wizard, which installs the software, open the XInstall window. To open the XInstall window 1. Log in to the computer as an administrator. If you are installing the software, you must be a software administrator. 2. Insert the Proteome Discoverer software DVD into the data system computer. If the auto-play is set for the DVD drive, the XInstall installation window appears automatically, as shown in Figure 1. Thermo Scientific Proteome Discoverer Installation Guide 1

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 1. XInstall window If this window does not appear, use Windows Explorer to open the installation file. In the Windows Explorer window, select the appropriate DVD drive and double-click the XInstall_ProteomeDiscoverer.exe file. Installing the Proteome Discoverer Software with an Internet Connection Use the Proteome Discoverer InstallShield wizard to install the software. IMPORTANT The following procedure assumes that you have already installed Microsoft.NET Framework 3.5 or 4.0 on your computer. If you do not have Microsoft.NET Framework 3.5 or 4.0 installed on your computer, install it before you install Proteome Discoverer 1.4 (you can install both of them from XInstall). Click Microsoft.NET Framework in the XInstall window shown in Figure 1 and complete the pages of the wizard. If you do not have the Microsoft Visual C++ 2010 and 2008 Redistributables installed on your computer, the Microsoft Visual C++ 2010 Redistributable wizard appears at the end of the Proteome Discoverer installation procedure, as shown in Figure 12 on page 13. Complete the pages of the wizard to install Microsoft Visual C++ 2010 Redistributable. 2 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection To install Proteome Discoverer 1. In the XInstall window, click Proteome Discoverer 1.4 software. The installer automatically recognizes whether the operating system is 32-bit or 64-bit and installs the appropriate version. The Proteome Discoverer InstallShield wizard appears, as shown in Figure 2. Figure 2. Welcome page of the Proteome Discoverer InstallShield wizard 2. Click Next to continue. The Minimum Product Requirements page appears, as shown in Figure 3. The installer checks the minimum system requirements, issuing an error message and terminating if one of the requirements is not met. Correct the error before continuing. If some of the settings are not optimal, the installer issues a warning message but continues. Thermo Scientific Proteome Discoverer Installation Guide 3

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 3. Minimum Product Requirements page of the Proteome Discoverer InstallShield wizard 3. Click Next. The License Agreement page appears, as shown in Figure 4. 4 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 4. License Agreement page of the Proteome Discoverer InstallShield wizard 4. Read the license agreement, select the I Accept the Terms of License Agreement option, and click Next. 5. On the Thermo License Activation page of the wizard, shown in Figure 5, enter your Proteome Discoverer product key. Also enter your complete and correct contact information, which is necessary for registering you correctly on the licensing server. The product key is in xxxx-xxxx-xxxx-xxxx format. You can find it on the DVD jewel case. Thermo Scientific Proteome Discoverer Installation Guide 5

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 5. Thermo License Activation page of the Thermo Discoverer InstallShield wizard 6. Click Activate. The Proteome Discoverer application retrieves your permanent license from the licensing server and licenses your software. The installation continues. If you incorrectly complete one of the fields in the Thermo License Activation dialog box, a red exclamation point appears next to it. Move the cursor over it to see an explanation of the error, as shown in Figure 6. Correct the error before you continue with the installation process. 6 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 6. Error ToolTip Note In the case of an update, the installer checks for a valid Proteome Discoverer installation before you can continue. Tip If you need help in installing or licensing the software, click Export the License Request in the Thermo License Activation dialog box, save that file, and contact licenses.ms@thermo.com with a short description of the issue. Attach the file. If you are installing an update on a new computer, contact your support organization, or send an e-mail to licenses.ms@thermo.com and include your original product key and your upgrade product key. Thermo Fisher Scientific provides you with a new product key that allows you to install the update directly. 7. Click OK to continue the setup process. The Choose Destination Location page opens, as shown in Figure 7. Thermo Scientific Proteome Discoverer Installation Guide 7

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 7. Choose Destination Location page of the Proteome Discoverer InstallShield wizard 8. Click Next. The Desktop Shortcuts page opens, as shown in Figure 8. 8 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 8. Desktop Shortcuts page of the Proteome Discoverer InstallShield wizard 9. If you want to create a Proteome Discoverer software shortcut on your desktop, select the Yes option and then click Next. The Select Program Folder page opens, as shown in Figure 9. Thermo Scientific Proteome Discoverer Installation Guide 9

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 9. Select Program Folder page of the Proteome Discoverer InstallShield wizard 10. Enter a different program folder name or select Thermo Proteome Discoverer 1.4 and click Next. The Start Copying Files page opens, as shown in Figure 10. 10 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 10. Start Copying Files page of the Proteome Discoverer InstallShield wizard 11. Click Back to review all settings or Next to start the installation. When you click Next, the system begins to install the Proteome Discoverer software. During the installation, the Setup Status page shown in Figure 11 displays the status of the installation. Thermo Scientific Proteome Discoverer Installation Guide 11

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 11. Setup Status page of the Proteome Discoverer InstallShield wizard 12. Do one of the following: If you need to terminate the installation of the Proteome Discoverer software setup, click Cancel. If you do not have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, look for the Welcome page of the Microsoft Visual C++ 2008 Redistributable wizard to appear (see Figure 12), and follow the procedure to install the Microsoft Visual C++ 2008 and 2010 Redistributables. or If you do have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, the Installation Qualification message box shown in Figure 16 on page 15 appears. Go to step 18. 12 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 12. Welcome page of the Microsoft Visual C++ Redistributable Setup wizard The Microsoft Visual C++ Redistributable Setup wizard first installs the 2008 version of the Microsoft Visual C++ Redistributable software, and then it installs the 2010 version. 13. Click Next. The License Terms page of the wizard opens, as shown in Figure 13. Thermo Scientific Proteome Discoverer Installation Guide 13

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection Figure 13. License Terms page of the Microsoft Visual C++ Redistributable Setup wizard 14. Make sure to accept the license terms, and then click Install. The Setup Complete page opens, as shown in Figure 14, Figure 14. Setup Complete page of the Microsoft Visual C++ Redistributable Setup wizard 14 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software with an Internet Connection 15. Click Finish. The Welcome page of the Microsoft Visual C++ 2010 x86 Redistributable Setup page of the wizard appears. 16. Repeat step 13 on page 13 through step 15 for the Microsoft Visual C++ 2010 Redistributable Setup. The warning message shown in Figure 15 appears, prompting you to permit the Proteome Discoverer application to gain access through the firewall. Figure 15. Firewall warning message Note This warning also appears the first time that you start the application. 17. Click Allow Access. After finishing the Proteome Discoverer software setup, the system creates the Installation Qualification report. Figure 16 shows the Installation Qualification message box with the report location. Figure 16. Installation Qualification message box 18. To view the report, click Yes. Otherwise, click No to end the installation. Thermo Scientific Proteome Discoverer Installation Guide 15

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software Without an Internet Connection Clicking Yes opens the Installation Qualification report as a PDF file. Clicking No opens the message box shown in Figure 17. Figure 17. Setup Finished message box 19. Click OK to exit the setup. IMPORTANT Ensure that port 28199 is not blocked by firewalls. The DVD also includes example raw files. Click Browse DVD on the Xinstall window (see Figure 1 on page 2) to access those files. Installing the Proteome Discoverer Software Without an Internet Connection If you do not have an Internet connection, use following procedure to install the Proteome Discoverer software. To install the Proteome Discoverer software without an Internet connection 1. Click Export the License Request on the Thermo License Activation dialog box (see Figure 5 on page 6), save the licensing file, and remove the DVD from the computer. Leave the Thermo License Activation dialog box open. 2. Copy the licensing file and move it to a computer with an Internet connection. Insert the Proteome Discoverer software DVD into that computer. The Xinstall window appears again (see Figure 1 on page 2). 3. Click Offline Activation. The Thermo License Activation dialog box, shown in Figure 5 on page 6, appears again with all its boxes empty. The Import License Activation Request dialog box also appears. 4. Browse to the license request file that you moved, and click Open. 5. Enter the appropriate information in all the boxes again. Note Ensure that the license request file is not write-protected. 6. Click Activate. 16 Proteome Discoverer Installation Guide Thermo Scientific

1 Installing Proteome Discoverer Installing the Proteome Discoverer Software Without an Internet Connection The Proteome Discoverer application activates the license and stores it in the license request file. 7. Click OK when the following message appears: Activation was successful. 8. Close the XInstall application window. 9. Copy the license request file, and move the file and the software DVD back to the computer that you want to license. The Thermo License Activation dialog box remains open. 10. Click Reimport the Activated License Request to Continue Activation. 11. Browse to the activated license request file. Thermo Scientific Proteome Discoverer Installation Guide 17

2 Installing Proteome Discoverer Daemon This chapter describes how to install the Proteome Discoverer Daemon software. Contents Opening the XInstall Window Installing the Proteome Discoverer Daemon Software Opening the XInstall Window Before you can access the Proteome Discoverer Daemon InstallShield wizard, which installs the software, you must open the XInstall window. For instructions on this procedure, see Opening the XInstall Window on page 1. If the auto-play is set for the DVD drive after you finish the procedure, the XInstall installation window appears automatically, as shown in Figure 18. Thermo Scientific Proteome Discoverer Installation Guide 19

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 18. XInstall window If this window does not appear, use Windows Explorer to open the installation file. In the Windows Explorer window, select the appropriate DVD drive and double-click the XInstall_ProteomeDiscoverer.exe file. Installing the Proteome Discoverer Daemon Software Use the Proteome Discoverer Daemon InstallShield wizard to install the software. IMPORTANT The following procedure assumes that you have already installed Microsoft.NET Framework 3.5 or 4.0 on your computer. If you have not, see Installing the Proteome Discoverer Software with an Internet Connection on page 2 for instructions. Note The following procedure is intended for installing the Proteome Discoverer Daemon 1.4 client on a machine separate from the machine where the Proteome Discoverer application is installed. By default, Proteome Discoverer Daemon 1.4 is installed during each Proteome Discoverer 1.4 installation. To install Proteome Discoverer Daemon 1. In the XInstall window, click Proteome Discoverer Daemon 1.4. The installer automatically recognizes whether the operating system is 32-bit or 64-bit and installs the appropriate version. 20 Proteome Discoverer Installation Guide Thermo Scientific

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software The Proteome Discoverer Daemon InstallShield wizard shown in Figure 19 appears. Figure 19. Welcome page of the Thermo Proteome Discoverer Daemon InstallShield wizard 2. Click Next to continue. The Minimum Product Requirements page appears, as shown in Figure 20. The installer checks the minimum system requirements, issuing an error message and terminating if one of the requirements is not met. Correct the error before continuing. If some of the settings are not optimal, the installer issues a warning message but continues. Thermo Scientific Proteome Discoverer Installation Guide 21

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 20. Minimum Product Requirements page of the Proteome Discoverer Daemon InstallShield wizard 3. Click Next. The License Agreement page of the Proteome Discoverer Daemon InstallShield wizard appears, as shown in Figure 21. 22 Proteome Discoverer Installation Guide Thermo Scientific

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 21. License Agreement page of the Proteome Discoverer Daemon InstallShield wizard 4. Read the license agreement. Select the I Accept the Terms of License Agreement option, and click Next. The Choose Destination Location page opens, as shown in Figure 22. Thermo Scientific Proteome Discoverer Installation Guide 23

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 22. Choose Destination Location page of the Proteome Discoverer Daemon InstallShield wizard 5. Do the following: To copy all needed files to the default location of C:\Program Files\ Thermo\DiscovererDaemon 1.4, click Next. or To copy all needed files to a different location, click Browse to browse to that location, and then click Next. The Desktop Shortcuts page opens, as shown in Figure 23. 24 Proteome Discoverer Installation Guide Thermo Scientific

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 23. Desktop Shortcuts page of the Proteome Discoverer Daemon InstallShield wizard 6. If you want to create a Proteome Discoverer Daemon shortcut on your desktop, select the Yes option and then click Next. The Select Program Folder page opens, as shown in Figure 24. Thermo Scientific Proteome Discoverer Installation Guide 25

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 24. Select Program Folder page of the Proteome Discoverer Daemon InstallShield wizard 7. Enter a different program folder name or select Thermo Proteome Discoverer 1.4 and click Next. The Start Copying Files page opens, as shown in Figure 25. 26 Proteome Discoverer Installation Guide Thermo Scientific

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 25. Start Copying Files page of the Proteome Discoverer Daemon InstallShield wizard 8. Click Back to review all settings or Next to start the installation. When you click Next, the system begins to install the Proteome Discoverer Daemon 1.4 software. During the installation, the Setup Status page shown in Figure 26 displays the status of the installation. Thermo Scientific Proteome Discoverer Installation Guide 27

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 26. Setup Status page of the Proteome Discoverer Daemon InstallShield wizard 9. Do one of the following: If you must terminate the installation of the Proteome Discoverer Daemon 1.4 setup, click Cancel. If you do not have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, look for the Welcome page of the Microsoft Visual C++ 2008 Redistributable wizard to appear (see Figure 12 on page 13), and follow the procedure to install the Microsoft Visual C++ 2008 and 2010 Redistributables. or If you do have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, the Installation Qualification message box shown in Figure 27 on page 29 appears. Go to step 10. After finishing the Proteome Discoverer Daemon setup, the system creates the Installation Qualification report. Figure 27 shows The Installation Qualification message box with the report location. 28 Proteome Discoverer Installation Guide Thermo Scientific

2 Installing Proteome Discoverer Daemon Installing the Proteome Discoverer Daemon Software Figure 27. Installation Qualification message box 10. To view the report, click Yes. Otherwise, click No to end the installation. Clicking Yes opens the Installation Qualification report as a PDF file. Clicking No opens the InstallShield Wizard Complete page, shown in Figure 28. Figure 28. InstallShield Wizard Complete page of the Thermo Discoverer Daemon InstallShield wizard 11. Click Finish to exit the setup. IMPORTANT Ensure that port 28199 is not blocked by firewalls. Thermo Scientific Proteome Discoverer Installation Guide 29

3 Installing Proteome Discoverer Viewer When you do a complete installation of the Proteome Discoverer 1.4 application, you automatically install Proteome Discoverer Viewer 1.4 software. This chapter describes how to install the Proteome Discoverer Viewer 1.4 software if you just want to view report results but do not want to install the Proteome Discoverer 1.4 application. Contents Opening the XInstall Window Installing the Proteome Discoverer Viewer Software Opening the XInstall Window Before you can access the Proteome Discoverer InstallShield wizard, which installs the Proteome Discoverer Viewer software, you must open the XInstall window. For instructions, see Opening the XInstall Window on page 1. If auto-play is set for the DVD drive after you finish the procedure, the XInstall installation window appears automatically, as shown in Figure 29. Thermo Scientific Proteome Discoverer Installation Guide 31

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 29. XInstall window If this window does not appear, use Windows Explorer to open the installation file. In the Windows Explorer window, select the appropriate DVD drive and double-click the XInstall_ProteomeDiscoverer.exe file. Installing the Proteome Discoverer Viewer Software Use the Proteome Discoverer InstallShield wizard to install the Proteome Discoverer Viewer software. IMPORTANT The following procedure assumes that you have already installed Microsoft.NET Framework 3.5 or 4.0 on your computer. If you have not, install them before proceeding. See Installing the Proteome Discoverer Software with an Internet Connection on page 2 for instructions. Note You must have access to the Internet to install the Proteome Discoverer Viewer. To install Proteome Discoverer Viewer 1. In the XInstall window, click Proteome Discoverer Viewer 1.4. The installer automatically recognizes whether the operating system is 32-bit or 64-bit and installs the appropriate version. The Proteome Discoverer InstallShield wizard shown in Figure 30 appears. 32 Proteome Discoverer Installation Guide Thermo Scientific

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 30. Welcome page of the Proteome Discoverer InstallShield wizard The installer checks the minimum system requirements, issuing an error message and terminating if one of the requirements is not met. Correct the error before continuing. If some of the settings are not optimal, the installer issues a warning message but continues. 2. Click Next to continue. The Minimum Product Requirements page of the Thermo Discoverer InstallShield wizard opens, as shown in Figure 31. Thermo Scientific Proteome Discoverer Installation Guide 33

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 31. Minimum Product Requirements page of the Thermo Discoverer InstallShield wizard The License Agreement page of the Thermo Discoverer InstallShield wizard opens, as shown in Figure 32. 34 Proteome Discoverer Installation Guide Thermo Scientific

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 32. License Agreement page of the Thermo Discoverer InstallShield wizard 3. Read the license agreement. If you accept the agreement, select the I Accept the Terms of License Agreement option, and click Next. 4. On the Thermo License Activation page of the wizard, shown in Figure 5 on page 6, enter your Proteome Discoverer product key. Also enter your complete and correct contact information, which is necessary for registering you correctly on the licensing server. The product key is in xxxx-xxxx-xxxx-xxxx format. You can find it on the DVD jewel case. Thermo Scientific Proteome Discoverer Installation Guide 35

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 33. Thermo License Activation page of the Proteome Discoverer InstallShield wizard 5. Click Activate. Note Viewer installations do not affect the product key, but Thermo Fisher Scientific strongly recommends that you install the full Proteome Discoverer 1.4 version first to avoid inadvertently installing it on the wrong computer when you only intend to install the Proteome Discoverer Viewer. 6. Click OK when the following message appears: Activation was successful. The Choose Destination Location page opens, as shown in Figure 34. 36 Proteome Discoverer Installation Guide Thermo Scientific

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 34. Choose Destination Location page of the Thermo Discoverer InstallShield wizard 7. Do the following: To copy all needed files to the default location of C:\Program Files\Thermo\Discoverer Viewer 1.4, click Next. or To copy all needed files to a different location, click Browse to browse to that location, and then click Next. The Desktop Shortcuts page opens, as shown in Figure 35. Thermo Scientific Proteome Discoverer Installation Guide 37

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 35. Desktop Shortcuts page of the Proteome Discoverer InstallShield wizard 8. If you want to create a Proteome Discoverer Viewer 1.4 shortcut on your desktop, select the Yes option and then click Next. The Select Program Folder page opens, as shown in Figure 36. 38 Proteome Discoverer Installation Guide Thermo Scientific

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 36. Select Program Folder page of the Proteome Discoverer InstallShield wizard 9. Enter a different program folder name or select Thermo Proteome Discoverer Viewer 1.4 and click Next. The Start Copying Files page opens, as shown in Figure 37. Thermo Scientific Proteome Discoverer Installation Guide 39

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 37. Start Copying Files page of the Thermo Discoverer InstallShield wizard 10. Click Back to review all settings or Next to start the installation. When you click Next, the system begins to install the Proteome Discoverer Viewer 1.4 software. During the installation, the Setup Status page shown in Figure 38 displays the status of the installation. 40 Proteome Discoverer Installation Guide Thermo Scientific

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 38. Setup Status page of the Proteome Discoverer InstallShield wizard 11. Do one of the following: If you need to terminate the installation of the Proteome Discoverer Viewer 1.4 setup, click Cancel. If you do not have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, look for the Welcome page of the Microsoft Visual C++ 2008 Redistributable wizard to appear (see Figure 12 on page 13), and follow the procedure to install the Microsoft Visual C++ 2008 and 2010 Redistributables. or If you do have Microsoft Visual C++ 2008 or 2010 Redistributable installed on your computer, the Installation Qualification message box shown in Figure 39 on page 42 appears. Go to step 12. After finishing the Proteome Discoverer setup, the system creates the Installation Qualification report. Figure 39 shows the Installation Qualification message box with the report location. Thermo Scientific Proteome Discoverer Installation Guide 41

3 Installing Proteome Discoverer Viewer Installing the Proteome Discoverer Viewer Software Figure 39. Installation Qualification message box 12. To view the report, click Yes. Otherwise, click No to end the installation. Clicking Yes opens the Installation Qualification report as a PDF file. Clicking No opens the message box shown in Figure 40. Figure 40. Setup Finished message box 13. Click OK to exit the setup. 42 Proteome Discoverer Installation Guide Thermo Scientific

4 Connecting to the Mascot Server This chapter describes Mascot server versions supported by the Proteome Discoverer software and how to check your Mascot server settings, connect to the Mascot server, and test the connection to the Mascot server. Contents Mascot Server Versions Supported Checking Your Mascot Server Settings Configuring Mascot Testing the Connection to the Mascot Server Mascot Server Versions Supported The Mascot server versions that the Proteome Discoverer software supports are as follows: Mascot Server 2.1 Mascot servers running version 2.1 should be usable, but retrieving the result files (protein sequences) from the servers can be a lengthy process, as you can only retrieve the protein sequences one by one. Mascot servers running version 2.1 should have all available updates, patches, or both from Matrix Science installed. In particular, you must install a patch that enables MIME format for the result files. Otherwise, the Proteome Discoverer software is not able to receive the search results from the Mascot server. Mascot Server 2.2 Proteome Discoverer 1.4 does not support error tolerant searches. Mascot Server 2.3 Proteome Discoverer 1.4 does not support error tolerant searches and searches against a multiple-sequence database. Thermo Scientific Proteome Discoverer Installation Guide 43

4 Connecting to the Mascot Server Checking Your Mascot Server Settings Checking Your Mascot Server Settings Checking the URL Before you connect to your Mascot server, verify that the URL of the Mascot server is valid, and determine what type of security protects your Mascot server. Check the Mascot server URL to be used in the Proteome Discoverer configuration by typing it into a Web browser. If the URL is correct, the Mascot home page appears. The URL of the Mascot server has the following general form: http://my.mascotserver.com/mascot/ If your Mascot server is not running on the standard port 80, you must include the actual port number: http://my.mascotserver.com:xxxx/mascot/ The Mascot server URL to be used in the Proteome Discoverer configuration does not include /cgi or /home.html or similar notation. The following are examples of invalid URLs: http://my.mascotserver.com/mascot/cgi http://my.mascotserver.com/mascot/home.html The following are examples of valid URLs: http://my.mascotserver.com/mascot/ http://192.168.2.1/mascot/ Checking for Security Options http://my.mascotserver.com:8765/mascot/ Check to see if your Mascot server is protected by security options and if so, by what type. If you are required to log in to the Mascot server or to log in through the Mascot Security page, shown in Figure 41, your Mascot server is protected by Mascot security. For information on accessing the Mascot server protected by this type of security, see To configure Mascot when your Mascot server is protected by Mascot security on page 47. 44 Proteome Discoverer Installation Guide Thermo Scientific

4 Connecting to the Mascot Server Configuring Mascot Figure 41. Mascot Security page If you must log in through any other means, your Mascot server is likely protected by the security options of the Web server that runs Mascot. For information on accessing the Mascot server protected by this type of security, see To configure Mascot when your Mascot server is protected by Windows or Web-based security on page 47. If you do not known which kind of security is enabled for your Mascot server, contact your local system administrator. Configuring Mascot You can configure Mascot in the Proteome Discoverer application by using any of the following three methods: Enter the Mascot server URL into the Configuration view. If your Mascot server is protected by Mascot security, use the values in the Mascot Server Authentication area of the Configuration view. The Proteome Discoverer application uses these values to connect to the Mascot server. Make sure that you have the appropriate access rights to the Mascot server. These access rights are directly configured on the Mascot server. If you need help in obtaining these access rights, contact your system administrator. Thermo Scientific Proteome Discoverer Installation Guide 45

4 Connecting to the Mascot Server Configuring Mascot If your Mascot server is protected by Web-based security, use the values in the Web Server Authentication area of the Configuration view. The Proteome Discoverer application uses these values to connect to the Mascot server. Make sure that you have the appropriate access rights to the Mascot server. These access rights are directly configured on the Mascot server. If you need help in obtaining these access rights, contact your system administrator. The following procedures detail these three methods. To configure Mascot through URL verification 1. Open the Proteome Discoverer application. 2. Choose Administration > Configuration > Mascot. 3. In the Mascot Server URL box in the Mascot Server area of the Configuration view, enter the URL of the Mascot server, as shown in Figure 42. Figure 42. Entering the Mascot server URL in the Mascot Server URL box 4. Click in another part of the interface. 46 Proteome Discoverer Installation Guide Thermo Scientific

4 Connecting to the Mascot Server Testing the Connection to the Mascot Server The Proteome Discoverer application checks the URL. If the URL is valid, the Proteome Discoverer application connects with the Mascot server. If the URL is invalid or if the application cannot reach it, the error message shown in Figure 43 appears. Figure 43. Invalid URL message box To configure Mascot when your Mascot server is protected by Mascot security 1. Open the Proteome Discoverer application. 2. Choose Administration > Configuration > Mascot. 3. In the Mascot Server Authentication area of the Configuration view, enter your user name in the User Name box and your password in the Password box to access the Web server hosting the specified Mascot server. To configure Mascot when your Mascot server is protected by Windows or Web-based security 1. Open the Proteome Discoverer application. 2. Choose Administration > Configuration > Mascot. 3. In the Web Server Authentication area of the Configuration view, enter your user name in the User Name box and your password in the Password box to access the Web server hosting the specified Mascot server. Testing the Connection to the Mascot Server This section explains how to test the connection between the Proteome Discoverer application and the Mascot server. To test the connection to the Mascot server 1. Start the Mascot Communication Tester by choosing Tools > Mascot Communication Tester. The Mascot Communication Tester window appears, as shown at the top of Figure 44. The Proteome Discoverer application automatically populates the fields of the window, including the URL in the Mascot Server Url box. Thermo Scientific Proteome Discoverer Installation Guide 47

4 Connecting to the Mascot Server Testing the Connection to the Mascot Server 2. If the URL does not automatically appear or you want to enter it manually, enter the URL of the Mascot server in the Mascot Server Url box. This is the same URL that you entered in the Mascot Server URL box in the Configuration view of the Proteome Discoverer application. If the Web server that hosts the Mascot server enables any user authentication, provide a user name and a password for this authentication in the corresponding boxes in the Mascot Communication Tester window. 3. Click Test Communication. An automated communication test starts, as shown in Figure 44. Figure 44. Test running in the Mascot Communication Tester window The upper pane displays the progress of the communication test, and the lower pane provides detailed information. When errors occur, the lower pane displays the particular test that failed, which helps you determine why the connection failed. You can click the blue highlighted links shown in the lower pane to test whether the communication works from within a Web browser. If this information does not resolve the problem, use the Copy Info button to copy the log information into an e-mail and send it to Thermo Fisher Scientific Customer Service at the e-mail address given in Contacting Us on page vii. 48 Proteome Discoverer Installation Guide Thermo Scientific

5 Submitting a Product Change Request Before submitting a product change request (also called a bug report), read the Known Issues section of the release notes and determine if any of the known issues describes your problem. If none of them do, file a product change request that includes all of the following information: The severity of the issue Whether the issue is already known Whether a solution is already available As many details as possible, including screen captures of the steps needed to duplicate this problem. If possible, provide some test data, such as MSF files or RAW files. To create a product change request 1. Choose Tools > Create Bug Report. The Proteome Discoverer Bug Reporter window opens. 2. Click Create Bug Report. The Proteome Discoverer application creates the bug report shown in Figure 45 and creates a ZIP file of the files in the \release directory. Figure 46 shows some of these files. Thermo Scientific Proteome Discoverer Installation Guide 49

5 Submitting a Product Change Request Figure 45. Proteome Discoverer Bug Reporter window Figure 46. Bug report 3. Send an e-mail to the product team and attach the ZIP file to the e-mail. 50 Proteome Discoverer Installation Guide Thermo Scientific

I Index B bug reports. See product change requests C Choose Destination Location page of the Proteome Discoverer InstallShield wizard 7, 36 Choose Destination Location page of the Thermo Proteome Discoverer Daemon InstallShield wizard 23 contacting us vii D Desktop Shortcuts page of the Proteome Discoverer InstallShield wizard 8, 37 Desktop Shortcuts page of the Thermo Proteome Discoverer Daemon InstallShield wizard 24 documentation survey vii E Export the License Request option 7, 16 F firewalls vi, 15 16, 29 I Installation Qualification message box 12, 28, 41 Installation Qualification report 15 InstallShield Wizard Complete page of the Thermo Proteome Discoverer Daemon InstallShield wizard 29 InstallShield wizard. See Proteome Discoverer Installshield wizard L license agreement 4, 22, 34 License Agreement page of the Proteome Discoverer InstallShield wizard 4, 34 License Agreement page of the Thermo Proteome Discoverer Daemon InstallShield wizard 22 License Terms page of the Microsoft Visual C++ Redistributable wizard 13 M Mascot configuring by verifying URL 45 46 configuring for Mascot security 45, 47 configuring for Web-based security 46 47 configuring in Proteome Discoverer application 45 Mascot Communication Tester 47 Mascot Security page 44 Mascot server checking for security options 44 checking settings 44 testing connection to Proteome Discoverer application 47 verifying URL 44 versions supported 43 Microsoft Visual C++ Redistributable software 2, 12, 28, 41 Microsoft Visual C++ Redistributable wizard 2008 12 2010 2 License Terms page 13 Setup Complete page 14 Welcome page 28, 41 Minimum Product Requirements page of the Proteome Discoverer InstallShield wizard 3, 33 Minimum Product Requirements page of the Thermo Proteome Discoverer Daemon InstallShield wizard 21 P product change requests 49 Proteome Discoverer installing 3 installing Proteome Discoverer Daemon 19 installing the Proteome Discoverer Viewer 31 installing without an Internet connection 16 Thermo Scientific Proteome Discoverer Installation Guide 51

Index: S InstallShield wizard 2 software required for installation 2 Proteome Discoverer Bug Reporter 49 Proteome Discoverer Daemon 19 Proteome Discoverer InstallShield wizard Choose Destination Location page 7, 36 Desktop Shortcuts page 8, 37 License Agreement page 4, 34 Minimum Product Requirements page 3, 33 Select Program Folder page 9, 38 Setup Status page 11, 40 Start Copying Files page 10, 39 Thermo License Activation page 5, 35 Welcome page 3, 33 Proteome Discoverer Viewer 31 W Welcome page of the Proteome Discoverer InstallShield wizard 3, 33 Welcome page of the Thermo Proteome Discoverer Daemon InstallShield wizard 21 X XInstall window 1, 19, 31 XInstall_ProteomeDiscoverer.exe 2, 20, 32 S Select Program Folder page of the Proteome Discoverer InstallShield wizard 9, 38 Select Program Folder page of the Thermo Proteome Discoverer Daemon InstallShield wizard 25 Setup Complete page of the Microsoft Visual C++ Redistributable wizard 14 Setup Finished message box 16, 42 Setup Status page of the Proteome Discoverer InstallShield wizard 11, 40 Setup Status page of the Thermo Proteome Discoverer Daemon InstallShield wizard 27 Start Copying Files page of the Proteome Discoverer InstallShield wizard 10, 39 Start Copying Files page of the Thermo Proteome Discoverer Daemon InstallShield wizard 26 survey link vii system requirements vi T Thermo License Activation page of the Proteome Discoverer InstallShield wizard 5, 35 Thermo Proteome Discoverer Daemon InstallShield wizard Choose Destination Location page 23 Desktop Shortcuts page 24 InstallShield Wizard Complete page 29 License Agreement page 22 Minimum Product Requirements page 21 Select Program Folder page 25 Setup Status page 27 Start Copying Files page 26 Welcome page 21 52 Proteome Discoverer Installation Guide Thermo Scientific